Continuity mistake: At One Eyed Jack's, when Agent Cooper and Jacques are sitting and talking there are 2 glasses of beer on the table. In one shot Jacques finishes a glass. When he gets up, both glasses are full. (00:10:20 - 00:11:40)
Other mistake: When Cooper is on the floor after being shot, as he's signing the check, he is doing so with the pen closed, and proceeds to click it open as he hands it back to the room service.
Continuity mistake: When Cooper is at the police station describing the events of the night of the murder, he is seen taking a doughnut and placing it on the napkin next to him. A few shots later his napkin is empty and the doughnut is back on the stack.
Continuity mistake: The position of Blackie's fingers on Audrey's chin switches depending on the angle. From behind, her fingers are straight; from the front, her fingers are scrunched up/bent.
Answer: The answer to pretty much any question beginning with "Has David Lynch ever explained _______?" is: no.